AUTHOR=Law Cherie Tsz-Yiu , Nivesvivat Thirapa , Xiong Qing , Kulkeaw Kasem , Shi Ling , Ruenchit Pichet , Suwanpakdee Detchvijitr , Suwanpakdee Piradee , Tongkrajang Nongnat , Sarasombath Patsharaporn T. , Tsui Stephen Kwok-Wing 

TITLE=Mitochondrial genome diversity of Balamuthia mandrillaris revealed by a fatal case of granulomatous amoebic encephalitis

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1162963

DOI=10.3389/fmicb.2023.1162963

ISSN=1664-302X

ABSTRACT=<sec><title>Introduction</title><p><italic>Balamuthia</italic> (<italic>B.</italic>) <italic>mandrillaris</italic> is a free-living amoeba that can cause rare yet fatal granulomatous amoebic encephalitis (GAE). However, efficacious treatment for GAE is currently unavailable, especially when genomic studies on <italic>B. mandrillaris</italic> are limited.</p></sec><sec><title>Methods</title><p>In this study, <italic>B. mandrillaris</italic> strain KM-20 was isolated from the brain tissue of a GAE patient, and its mitochondrial genome was <italic>de novo</italic> assembled using high-coverage Nanopore long reads and Illumina short reads.</p></sec><sec><title>Results and Discussion</title><p>Phylogenetic and comparative analyses revealed a range of diversification in the mitochondrial genome of KM-20 and nine other <italic>B. mandrillaris</italic> strains. According to the mitochondrial genome alignment, one of the most variable regions was observed in the ribosomal protein S3 (<italic>rps3</italic>), which was caused by an array of novel protein tandem repeats. The repeating units in the <italic>rps3</italic> protein tandem region present significant copy number variations (CNVs) among <italic>B. mandrillaris</italic> strains and suggest KM-20 as the most divergent strain for its highly variable sequence and highest copy number in <italic>rps3</italic>. Moreover, mitochondrial heteroplasmy was observed in strain V039, and two genotypes of <italic>rps3</italic> are caused by the CNVs in the tandem repeats. Taken together, the copy number and sequence variations of the protein tandem repeats enable <italic>rps3</italic> to be a perfect target for clinical genotyping assay for <italic>B. mandrillaris</italic>. The mitochondrial genome diversity of <italic>B. mandrillaris</italic> paves the way to investigate the phylogeny and diversification of pathogenic amoebae.</p></sec>